Reagents and methods for detecting protein lysine 2-hydroxyisobutyrylation

ABSTRACT

The invention provides an isolated peptide comprising a lysine 2-hydroxyisobutyrylation site, a lysine 2-hydroxyisobutyrylation specific affinity reagent that specifically binds to the peptide, and a method for detecting protein lysine 2-hydroxyisobutyrylation in a sample using the reagent.

REFERENCE TO U.S. GOVERNMENT SUPPORT

This work is supported by a grant from the National Institute of Health (Grant Nos. DK082664 and RR020389). The United States has certain rights in the invention.

FIELD OF THE INVENTION

This invention relates to reagents and methods for detecting proteins having post-translational modifications. More particularly, it relates to peptides comprising a 2-hydroxyisobutyrylated lysine, and their uses to develop reagents and methods useful for detecting protein lysine 2-hydroxyisobutyrylation.

BACKGROUND OF THE INVENTION

Chromatin is decorated with a wide variety of protein post-translational modifications (PTMs), such as acetylation, methylation, phosphorylation and recently β-N-acetylglucosamine (O-GlcNAc) modifications. The regulatory potential of histone marks is well illustrated for histone lysine acetylation (K_(ac)) and lysine methylation. Small chemical differences at a given lysine residue, e.g., acetylation vs methylation, may associate with very different functional outputs. Moreover, subtle differences within the same family of modifications can be of functional significance. For instance, lysine methylation can be present in three forms: mono-, di- or tri-methylation. Depending on the methylation state and its position, histone lysine methylation can be involved in either the activation or repression of gene expression. For example, lysine monomethylation and lysine trimethylation of histone H3K4 respectively mark enhancers and promoters of active genes. The dysregulation of histone marks can lead to diverse diseases, such as cancer.

The differentiation of male germ cells offers a particularly interesting setting to explore the biological significance of new histone PTM. Indeed, during this process, the male genome undergoes several large-scale structural and functional changes, including the establishment of stage-specific expression patterns, and a genome-wide replacement of histones by transition proteins and protamines.

There remains a need for developing reagents and methods useful for detecting post-translational modifications of histones or nonhistone proteins linked to various diseases and disorders.

SUMMARY OF THE INVENTION

The present invention relates to the use of peptides comprising a 2-hydroxyisobutyrylated lysine (K_(2ohibu)) to develop reagents and methods for detecting protein lysine 2-hydroxyisobutyrylation, especially site specific lysine 2-hydroxyisobutyrylation.

An isolated peptide comprising a 2-hydroxyisobutyrylated lysine is provided. The isolated peptide may be derived from a histone protein or a fragment thereof. The histone protein may be derived from an organism selected from the group consisting of human, mouse, S. cerevisiae, Tetrahymena thermophila, D. melanogaster, and C. elegans. The isolated peptide may comprise an amino acid sequence having at least 70% identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 29-112. The isolated peptide may comprise an amino acid sequence selected from SEQ ID NOs: 29-112. The isolated peptide may comprise at least 2 amino acid residues on each of the N-terminal and C-terminal sides of the 2-hydroxyisobutyrylated lysine.

An isolated lysine 2-hydroxyisobutyrylation specific affinity reagent is also provided. It is capable of binding specifically to a peptide comprising a 2-hydroxyisobutyrylated lysine. The peptide may comprise an amino acid sequence selected from SEQ ID NOs: 29-112. The binding may be dependent on the presence of the 2-hydroxyisobutyrylated lysine but not a surrounding peptide sequence thereof in the peptide. The binding may be dependent on the presence of the 2-hydroxyisobutyrylated lysine and a surrounding peptide sequence thereof in the peptide. The lysine 2-hydroxyisobutyrylation specific affinity reagent may be a protein or an antibody.

A method for producing a lysine 2-hydroxyisobutyrylation specific affinity reagent that is a protein is provided. The method comprises screening a protein library using a peptide comprising a 2-hydroxyisobutyrylated lysine and at least two amino acid residues on each of the N-terminal and C-terminal sides of the 2-hydroxyisobutyrylated lysine. The protein library may be selected from the group consisting of a phage display library, a yeast display library, a bacterial display library, and a ribosome display library.

A method for producing a lysine 2-hydroxyisobutyrylation specific affinity reagent that is an antibody is also provided. The method comprises immunizing a host with a peptide comprising a 2-hydroxyisobutyrylated lysine and at least two amino acid residues on each of the N-terminal and C-terminal sides of the 2-hydroxyisobutyrylated lysine.

A method for detecting a 2-hydroxyisobutyrylated lysine in a protein or a fragment thereof is provided. The method comprises contacting the protein or a fragment thereof with the isolated lysine 2-hydroxyisobutyrylation specific affinity reagent capable of binding specifically to a peptide comprising a 2-hydroxyisobutyrylated lysine. The lysine 2-hydroxyisobutyrylation specific affinity reagent and the protein or a fragment thereof forms a binding complex. The method further comprise detecting the binding complex. The presence of the binding complex indicates the presence of a 2-hydroxyisobutyrylated lysine in the protein or a fragment thereof. In this method, the lysine 2-hydroxyisobutyrylation specific affinity reagent may be a protein or an antibody.

A method for determining the level of protein lysine 2-hydroxyisobutyrylation in a sample is provided. The method comprises detecting a 2-hydroxyisobutyrylated lysine in the sample.

A kit for detecting a 2-hydroxyisobutyrylated lysine in a protein of a fragment thereof is provided. The kit comprises an isolated lysine 2-hydroxyisobutyrylation specific affinity reagent capable of binding specifically to a peptide comprising a 2-hydroxyisobutyrylated lysine.

A kit for isolating a peptide containing a 2-hydroxyisobutyrylated lysine is also provided. The kit comprises an isolated lysine 2-hydroxyisobutyrylation specific affinity reagent capable of binding specifically to a peptide comprising a 2-hydroxyisobutyrylated lysine.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1 shows chemical structures of lysine, acetyllysine, and other possible chemical structures of lysine modifications that may have the elemental composition of C₄H₇O₂ and induce a mass shift of +86.0368 Da.

FIG. 2 shows verification of 2-hydroxyisobutyrylation at histone H4K77. (A) The MS/MS spectra of an in vivo peptide bearing a PTM (DAVTYTEHAK_(+86.0354)R) (DAVTYTEHAKR; SEQ ID NO: 29) (top), a synthetic lysine 2-hydroxyisobutyrylated peptide corresponding to the sequence of the in vivo peptide (middle), and a mixture of the two peptides (bottom). The label A designates b or y ions with water and/or ammonia loss. Insets show the precursor ion masses. (B) Extracted ion chromatograms (XICs) of a mixture of four synthetic peptides (DAVTYTEHAK_((±)-2ohbu)R, DAVTYTEHAK_((r)-3ohbu)R, DAVTYTEHAK_((s)-3ohibu)R and DAVTYTEHAK_(4ohbu)R) and the in vivo peptide. (C) Extracted ion chromatograms (XIC) of the in vivo peptide (top), the synthetic peptide DAVTYTEHAK_(2ohibu)R (middle), and the mixture of the both peptides (bottom).

FIG. 3 shows histone K_(2ohibu) in eukaryotic cells. (A) Western blotting analysis of the recombinant H4 and HeLa cell core histones. Immunoblot against H4 was used as a loading control. (B) Detection of K_(2ohibu) and H4K8_(2ohibu) in human HeLa cells, MEF cells, Drosophila S2 cells and yeast S. cerevisiae cells by Western blotting. (C) The K_(2ohibu) sites from lysine 34 to lysine 120 in histone H2B shown in 3D structure of mouse nucleosome. H2B in the nucleosome is in ribbon shape and the other histones are displayed as backbones. The K_(2ohibu) residues are highlighted in molecular ball shapes. (D) The lysine residues of all the K_(2ohibu) sites in human and mouse histones are shown in red and bold. The unique sites with K_(2ohibu), but without K_(cr) and K_(ac) being reported are labeled with underscore. To make a comparison, the known K_(ac) sites (labeled with a black triangle) and K_(cr) sites (labeled with a green star) described in the literature were also listed.

FIG. 4 shows spatiotemporal analyses of H4K8_(2ohibu) and H4K8_(ac) in mouse sperm cells. Sections from paraffin embedded testes were used for the detection of H4K8_(2ohibu) (A) and H4K8_(ac) (B) by immunohistochemistry (1H), with or without counterstaining. The tubule stages are indicated above each panel. The insets show a higher magnification of a dot-like structure observed in round spermatids. (C) Both H4K8_(2ohibu) and H4K8_(ac) marks are visualized by immunofluorescence (IF) in round spermatids from seminiferous tubule preparations. In each panel, the indicated PTMs (green) are co-detected along with HP1gamma (red).

FIG. 5 shows high-Resolution mapping of H4K8_(2ohibu) and H4K8_(ac) in spermatocytes (meiotic cells) and round spermatids (post-meiotic cells). (A) The upper panels show the distributions of H4K8_(2ohibu) (right) and H4K8_(ac) (left) peaks between the two cell populations (spermatocytes (Spc) and round spermatids (RS)), while the lower panels show the distributions of overlapped and unique peaks for H4K8_(2ohibu) and H4K8_(ac) in Spc (left) and RS (right). (B) Metagene analysis of H4K8_(2ohibu) and H4K8_(ac) peaks with respect to their associated genes' transcription starting site (TSS). Color code for cell types and the histone marks are indicated. TES means transcription end site. (C) and (D) Distributions per chromosome of H4K8_(ac) peaks (C) and H4K8_(2ohibu) peaks (D). Peaks observed in spermatocytes and spermatids are represented in blue and red, respectively. The sex chromosomes are highlighted to emphasize the evolution of peak intensities on these chromosomes between spermatocytes and round spermatids.

FIG. 6 shows that H4K8_(2ohibu) is associated with genes with high transcriptional activity in male germ cells. (A) Number of genes associated with H4K8_(2ohibu) and/or H4K8_(ac) peaks in male germ cells (spermatocytes and/or round spermatids). (B) Expression of genes associated with H4K8_(2ohibu) peaks in mouse tissues: distribution of H4K8_(2ohibu) associated genes according to their sites of predominant expression in mouse tissues. (C) Gene expression patterns of testis-specific genes associated with H4K8_(2ohibu) in spermatogenic cells: the heatmap shows the expression levels of H4K8_(2ohibu) associated genes with a testis predominant expression in meiotic cells (spermatocytes: Spc) and post-meiotic cells (round spermatids: RS). Color scale: from green (low expression) to red (high expression). (D) Box plots comparing the distribution of expression levels of genes associated with H4K8_(2ohibu) and/or H4K8_(ac) peaks in meiotic cells (Spermatocytes: Spc) and in post-meiotic cells (Round spermatids: RS). * p<0.001 (unpaired t-test) showing a significant difference with the reference group of genes (not associated with H4K8_(2ohibu) or H4K8_(ac) peaks); ** p<0.001 (unpaired t-test) showing a significant difference with all the other groups of genes including the reference group of genes (not associated with H4K8_(2ohibu) or H4K8_(ac) peaks) and the genes associated with either H4K8_(ac) or H4K8_(2ohibu) alone. (E) Proportions of X-linked genes and autosomal genes associated with H4K8_(2ohibu) (left panel) or H4K8_(ac) (right panel).

FIG. 7 shows protein sequences of human histone proteins (A) H1.2 (SEQ ID NO: 1), (B) H2A (SEQ ID NO: 2), (C) H2B (SEQ ID NO: 3), (D) H3 (SEQ ID NO: 4), and (E) H4 (SEQ ID NO: 5).

FIG. 8 shows protein sequences of mouse histone proteins (A) H1.2 (SEQ ID NO: 6), (B) H2A (SEQ ID NO: 7), (C) H2B (SEQ ID NO: 8), (D) H3 (SEQ ID NO: 9), and (E) H4 (SEQ ID NO: 10).

FIG. 9 shows protein sequences of S. cerevisiae histone proteins (A) H2A (SEQ ID NO: 11), (B) H2B (SEQ ID NO: 12), (C) H3 (SEQ ID NO: 13), and (D) H4 (SEQ ID NO: 14).

FIG. 10 shows protein sequences of Tetrahymena histone proteins (A) H2A (SEQ ID NO: 15), (B) H2B (SEQ ID NO: 16), (C) H3 (SEQ ID NO: 17), and (D) H4 (SEQ ID NO: 18).

FIG. 11 shows protein sequences of D. melanogaster histone proteins (A) H1 (SEQ ID NO: 19), (B) H2A (SEQ ID NO: 20), (C) H2B (SEQ ID NO: 21), (D) H3 (SEQ ID NO: 22), and (E) H4 (SEQ ID NO: 23).

FIG. 12 shows protein sequences of c. elegans histone proteins (A) H1 (SEQ ID NO: 24), (B) H2A (SEQ ID NO: 25), (C) H2B (SEQ ID NO: 26), (D) H3 (SEQ ID NO: 27), and (E) H4 (SEQ ID NO: 28).

DETAILED DESCRIPTION OF THE INVENTION

The present invention is based on the discovery of a new type of histone marks, lysine 2-hydroxyisobutyrylation. In particular, over 60 novel histone lysine 2-hydroxyisobutyrylation sites in human and mouse cells have been identified. Genome-wide mapping of histone H4 lysine 82-hydroxyisobutyrylation (H4K8_(2ohibu)), in parallel with histone H4 lysine 8 acetylation (H4K8_(ac)), in spermatogenic cells, shows that H4K8_(2ohibu) is a new indicator of gene transcriptional activity, demonstrating that lysine 2-hydroxyisobutyrylation represents a novel active histone mark with important functions in the physiological setting of male germ cell differentiation. Peptides derived from histone proteins or fragments thereof comprising a K_(2ohibu) site may be used to generate reagents useful for detecting protein lysine 2-hydroxyisobutyrylation, especially for detecting site specific protein lysine 2-hydroxyisobutyrylation.

The term “peptide” used herein refers to a linear chain of two or more amino acids linked by peptide bonds. A peptide may have about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 100, 200 or more amino acids. The amino acids of a peptide may be modified, deleted, added or substituted. A peptide may be obtained using conventional techniques known in the art. For example, a peptide may be synthesized or obtained from a native or recombinant protein by enzymatic digestion.

The term “polypeptide” used herein refers to a peptide having at least 4 amino acids, preferably at least about 20 amino acids, regardless of post-translational modification. The term “protein” used herein refers to a biological molecule consisting of one or more polypeptides, regardless of post-translational modification. Each polypeptide in a protein may be a subunit. The polypeptide or protein may be in a native or modified form, and may exhibit a biological function or characteristics.

Where a protein is a single polypeptide, the terms “protein” and “polypeptide” are used herein interchangeably. A fragment of a polypeptide or protein refers to a portion of the polypeptide or protein having an amino acid sequence that is the same as a part, but not all, of the amino acid sequence of the polypeptide or protein. Preferably, a fragment of a polypeptide or protein exhibits a biological function or characteristics identical or similar to that of the polypeptide or protein.

The term “derived from” used herein refers to the origin or source from which a biological molecule is obtained, and may include naturally occurring, recombinant, unpurified or purified molecules. A biological molecule such as a peptide (e.g., a polypeptide or protein) may be derived from an original molecule, becoming identical to the original molecule or a variant of the original molecule. For example, a peptide derived from an original peptide may have an amino acid sequence identical or similar to the amino acid sequence of its original peptide, with at least one amino acid modified, deleted, inserted, or substituted. A derived peptide may have an amino acid sequence at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99% or 100%, preferably at least about 50%, more preferably at least about 80%, most preferably at least about 90%, identical to the amino acid sequence of its original peptide, regardless of post-translational modification. Preferably, a derived biological molecule (e.g., a peptide) may exhibit a biological function or characteristics identical or similar to that of the original biological molecule.

The term “antibody” used herein includes whole antibodies, and antigen binding fragments (or antigen-binding portions) and single chains thereof. A whole antibody can be either one of the two types. The first type refers to a glycoprotein typically having two heavy chains and two light chains, and includes an antigen binding portion. For example, the antibody may be a polyclonal or monoclonal antibody. The term “antigen binding portion” of an antibody used herein refers to one or more fragments of the antibody that retain the ability of specifically binding to an antigen. The second type refers to a heavy-chain antibody occurring in camelids that is also called Nanobody. The term “single-chain variable fragment” of an antibody used herein refers to a fusion protein of the variable regions of the heavy and light chains of the antibody, connected with a short linker peptide, for example, of about 20-25 amino acids, that retains the ability of specifically binding to an antigen.

An isolated peptide comprising a 2-hydroxyisobutyrylated lysine is provided. The term “2-hydroxyisobutyrylated lysine” used herein refers to a lysine residue that is 2-hydroxyisobutyrylated on its epsilon-amine group. It is also known as a 2-hydroxyisobutyryl lysine residue. The term “lysine 2-hydroxyisobutyrylation site” used herein refers to a lysine residue in a peptide, polypeptide or protein that may be 2-hydroxyisobutyrylated on the epsilon-amine group of the lysine residue. The term “lysine 2-hydroxyisobutyrylation” used herein refers to 2-hydroxyisobutyrylation on the epsilon-amine group of a lysine residue that generates a 2-hydroxyisobutyryl lysine residue or 2-hydroxyisobutyrylated lysine.

The peptide of the present invention may have at least about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150 or 200 amino acids. The peptide may have about 3-25 amino acids, preferably 5-20 amino acids, more preferably 6-14 amino acids.

The peptide of the present invention may be prepared using conventional techniques known in the art. The peptide may be derived from a protein, for example, a histone protein, or a fragment thereof, having a lysine 2-hydroxyisobutyrylation site. The histone protein may be derived from a eukaryotic cell. Examples of a eukaryotic cell include cells from a yeast (e.g., S. cerevisiae), an C. elegans, a Drosophila (e.g., D. melanogaster (S2)), a Tetrahymena (e.g., Tetrahymena thermophila), a mouse (e.g., M. musculus (MEF)), or a human. Preferably, the eukaryotic cell is a mammalian cell, for example, a human, primate, mouse, rat, horse, cow, pig, sheep, goat, chicken, dog or cat cell. More preferably, the eukaryotic cell is a human cell.

The histone protein may be a histone linker protein or a histone core protein. A histone linker protein may be selected from the members of the H1 family, including the H1F subfamily (e.g., H1F0, H1FNT, H1FOO, and H1FX) and the H1H1 subfamily (e.g., HIST1H1A, HIST1H1B, HIST1H1C, HIST1H1D, HIST1H1E and HIST1H1T). A histone core protein may a member of the H2A, H2B, H3 or H4 family. A histone core protein in the H2A family may be a member of the H2AF subfamily (e.g., H2AFB1, H2AFB2, H2AFB3, H2AFJ, H2AFV, H2AFX, H2AFY, H2AFY2, and H2AFZ), the H2A1 subfamily (e.g., HIST1H2AA, HIST1H2AB, HIST1H2AC, HIST1H2AD, HIST1H2AE, HIST1H2AG, HIST1H2AH, HIST1H2AI, HIST1H2AJ, HIST1H2AK, HIST1H2AL, and HIST1H2AM), or the H2A2 subfamily (e.g., HIST2H2AA3, HIST2H2AA4, HIST2H2AB, and HIST2H2AC). A histone core protein in the H2B family may be a member of the H2BF subfamily (e.g., H2BFM and H2BFWT), the H2B1 subfamily (e.g., HIST1H2BA, HIST1H2BB, HIST1H2BC, HIST1H2BD, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BH, HIST1H2BI, HIST1H2BJ, HIST1H2BK, HIST1H2BL, HIST1H2BM, HIST1H2BN, and HIST1H2BO), or the H2B2 subfamily (e.g., HIST2H2BE and HIST2H2BF). A histone core protein in the H3 family may be a member of the H3A1 subfamily (e.g., HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, and HIST1H3J), the H3A2 subfamily (e.g., HIST2H3A, HIST2H3C, and HIST2H3D), or the H3A3 subfamily (e.g., HIST3H3), the H3A3 subfamily (e.g., H3F3A, H3F3B, and H3F3C). A histone core protein in the H4 family may be a member of the H41 subfamily (e.g., HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H₄F, HIST1H4G, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, and HIST1H4L), or the H44 subfamily (e.g., HIST4H4).

The protein and gene sequences of histone proteins in various species are known in the art. For example, protein sequences of human H1.2, H2A, H2B, H3 and H4 histone proteins can be found in GenBank database Accession Nos. P16403 (H12_HUMAN) having SEQ ID NO: 1 (FIG. 7A), P04908 (H2A1B_HUMAN) having SEQ ID NO: 2 (FIG. 7B), P33778 (H2B1B_HUMAN) having SEQ ID NO: 3 (FIG. 7C), P84243 (H33_HUMAN) having SEQ ID NO: 4 (FIG. 7D) and P62805 (H4_HUMAN) having SEQ ID NO: 5 (FIG. 7E) respectively. The protein sequences of mouse histone proteins H1.2, H2A, H2B, H3 and H4 can be found in the GenBank database Accession Nos. P15864 (H12_MOUSE) having SEQ ID NO: 6 (FIG. 8A), P22752 (H2A1_MOUSE) having SEQ ID NO: 7 (FIG. 8B), Q64475 (H2B1B_MOUSE) having SEQ ID NO: 8 (FIG. 8C), P84244 (H33_MOUSE) having SEQ ID NO: 9 (FIG. 8D) and P62806 (H4_MOUSE) having SEQ ID NO: 10 (FIG. 8E), respectively. Histone protein sequences of other species such as S. cerevisiae (FIG. 9), Tetrahymena (FIG. 10), D. melanogaster (FIG. 11), and C. elegans (FIG. 12) are also known.

A fragment of a histone protein may have an amino acid sequence that is the same as a part, not all, of the amino acid sequence of the histone protein comprising at least one lysine 2-hydroxyisobutyrylation site. The histone protein fragment may have at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150 or 200 amino acids. The histone fragment may have about 3-25 contiguous amino acids, preferably about 5-20 contiguous amino acids, more preferably about 6-14 contiguous amino acids, of the histone protein covering at least one lysine 2-hydroxyisobutyrylation site in the histone protein.

The histone protein or fragment may have a 2-hydroxyisobutyrylated lysine at a lysine 2-hydroxyisobutyrylation site. The lysine 2-hydroxyisobutyrylation site may be any one of the lysine 2-hydroxyisobutyrylation sites in exemplary histone proteins of human (Table 1), mouse (Table 2), S. cerevisiae (Table 3), and Tetrahymena (Table 4).

A histone protein may be obtained from a biological sample or prepared using recombinant techniques. A histone protein fragment may be prepared by recombinant techniques, or by digesting the histone protein with an enzyme (e.g., trypsin). The lysine 2-hydroxyisobutyrylation site in the histone protein or fragment may be lysine 2-hydroxyisobutyrylated naturally or artificially. The presence of a 2-hydroxyisobutyrylated lysine may be confirmed by using conventional techniques known in the art, for example, mass spectrometry.

The peptide of the present invention may comprise an amino acid sequence having at least about 70%, 80%, 90%, 95% or 99%, preferably at least about 90%, more preferably 100%, identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 29-112. The peptide may encompass any lysine 2-hydroxyisobutyrylation site with or without its surrounding sequences from a histone proteins. The peptide may comprise more than one 2-hydroxyisobutyrylated lysine. The peptide may also comprise a protein post-translational modification other than 2-hydroxyisobutyrylated lysine, such as acetylated lysine or methylated lysine. The peptides may further comprise at least about 1, 2, 3, 4, 5, 5, 6, 7, 8, 9, 10 or more residues on either or both of N-terminal and C-terminal sides of the 2-hydroxyisobutyrylated lysine. Preferably, the peptide may comprise at least 2 amino acid residues on each of the N-terminal and C-terminal side of the 2-hydroxyisobutyrylated lysine. Exemplary peptides of the present invention are shown in Tables 1-4.

An isolated lysine 2-hydroxyisobutyrylation specific affinity reagent is also provided. The term “lysine 2-hydroxyisobutyrylation specific affinity reagent” used herein refers to a molecule that is capable of binding to a peptide, polypeptide or protein having a lysine 2-hydroxyisobutyrylation site, which may be a histone protein or a peptide of the present invention. The lysine 2-hydroxyisobutyrylation specific affinity reagent may be a protein, for example, an antibody. The lysine 2-hydroxyisobutyrylation site may be any lysine 2-hydroxyisobutyrylation site in any histone protein from any species. Examples of the lysine 2-hydroxyisobutyrylation sites include those in human (Table 1), mouse (Table 2), S. cerevisiae (Table 3), and Tetrahymena (Table 4), and homologous lysine sites in corresponding eukaryotic histone proteins.

In some embodiments, the lysine 2-hydroxyisobutyrylation specific affinity reagent binds a peptide, polypeptide or protein having a lysine 2-hydroxyisobutyrylation site that is 2-hydroxyisobutyrylated, having an affinity that is at least about 10, 50, 100, 500, 1000 or 5000 times higher than that for its counterpart when the site is not 2-hydroxyisobutyrylated.

In other embodiments, the lysine 2-hydroxyisobutyrylation specific affinity reagent binds a peptide, polypeptide or protein having a lysine 2-hydroxyisobutyrylation site that is not 2-hydroxyisobutyrylated, having an affinity that is at least about 10, 50, 100, 500, 1000 or 5000 times higher than that for its counterpart when the site is 2-hydroxyisobutyrylated. The lysine 2-hydroxyisobutyrylation specific affinity reagent may be a peptide, polypeptide or protein, which may be an antibody. Preferably, the peptide is a peptide of the present invention.

The lysine 2-hydroxyisobutyrylation specific affinity reagent may be site specific, i.e., the binding is dependent on the presence of the 2-hydroxyisobutyrylated lysine and its surrounding peptide sequence. The surrounding peptide sequence may include at least about 1, 2, 3, 4, 5, 5, 6, 7, 8, 9, 10 or more residues on either or both of N-terminal and C-terminal sides of the 2-hydroxyisobutyrylated lysine. For example, the binding depends on the presence of the 2-hydroxyisobutyrylated lysine and at least 2 amino acid residues on each of the N-terminal and C-terminal side of the 2-hydroxyisobutyrylated lysine.

The lysine 2-hydroxyisobutyrylation specific affinity reagent may not be site specific, i.e., the binding is dependent on the presence of the 2-hydroxyisobutyrylated lysine but not its surrounding peptide sequence. One example is an anti-lysine-2-hydroxyisobutyrylation pan antibody.

A method for producing the lysine 2-hydroxyisobutyrylation specific affinity reagent of the present invention is further provided.

Where the lysine 2-hydroxyisobutyrylation specific affinity reagent is a protein, the protein may be produced by screening a protein library (also known as a display library or a degenerated protein library) using the peptide of the present invention. The peptide may have at least two amino acid residues one each of the N-terminal and C-terminal sides of the 2-hydroxyisobutyrylated lysine. The protein library may consist of many degenerated protein sequences, which may comprise two regions: one or more fixed peptide sequence regions and a plurality of degenerated amino acid sequences. The protein library may be a phage protein library, a yeast protein library, bacterial protein library, ribosome protein library, or other synthetic protein library comprising peptides having randomized amino acid sequences.

Where the lysine 2-hydroxyisobutyrylation specific affinity reagent is an antibody, the antibody may be produced by different methods known in the art. For example, the production method may comprise immunizing a host with an antigenic peptide to produce the antibody. The method may further comprise collecting antisera from the host. The host may be a mammal suitable for producing antibodies. For example, the host may be a mouse, rabbit, goat, Camelidae family animal (such as Lama and camel), or cartilaginous fishes. Dependent on the host used, the generated antibody can contain either two chains (a heavy chain and a light chain) or one chain (or heavy chain-only antibody occurring in cam(lids) that is also called Nanobody.

The antigenic peptide may be derived from a histone protein or a fragment thereof comprising a lysine 2-hydroxyisobutyrylation site, which may be 2-hydroxyisobutyrylated or not. The antigenic peptide may comprise a peptide of the present invention. Examples of antigenic peptides having 2-hydroxyisobutyrylated lysine may comprise one or more of the peptides in Tables 1 and 2. Examples of antigenic peptides not having 2-hydroxyisobutyrylated lysine may have an amino acid sequence identical to those in Tables 1 and 2, except that the lysine 2-hydroxyisobutyrylation site is not 2-hydroxyisobutyrylated. The N-terminal or C-terminal end of any of these peptides may be extended by 1-20 residues.

The method may further comprise purifying the antibody from the antisera. The method may further comprise utilizing spleen cells from the host to generate a monoclonal antibody. In some embodiments, the antibody specifically binds to a histone protein or fragment having a lysine 2-hydroxyisobutyrylation site when the site is 2-hydroxyisobutyrylated, but not when the site is not 2-hydroxyisobutyrylated. In other embodiments, the antibody specifically binds to a histone protein or fragment having a lysine 2-hydroxyisobutyrylation site when the site is not 2-hydroxyisobutyrylated, but not when the site is 2-hydroxyisobutyrylated.

The method may further comprise deduce the antibody sequences by high-performance liquid chromatography (HPLC)-mass spectrometry analysis of the isolated antibodies and followed by protein sequence database search against all the possible IgG protein sequences (derived from cDNA sequences) from bone marrow (or B cells) of the immunized host. The IgG cDNA sequences can be obtained from conventional DNA sequencing technologies from IgG cDNAs that are generated by RT-PCR using the known art. The derived heavy- and light-chain variable regions (VH and VL) can be further paired (in case the IgG is from a two-chain antibodies from a host like mice or rabbit). Such a pairing is not necessary for those IgG derived from heavy chain-only antibody (or Nonabody) from Lama. The antibody can then be generated using the antibody sequence information using the known art.

A method for detecting a 2-hydroxyisobutyrylated lysine in a protein or its fragment is provided. The method comprises (a) contacting the protein or its fragment with a lysine 2-hydroxyisobutyrylation specific affinity reagent of the present invention to form a binding complex, and (b) detecting the binding complex. The presence of the binding complex indicates the presence of the 2-hydroxyisobutyrylated lysine in the protein or its fragment. The binding complex may be detected by using various conventional methods in the art. The protein may be a histone protein. The method may further comprise quantifying the amount of the binding complex. The amount of the binding complex may indicate the level of lysine 2-hydroxyisobutyrylation in the protein or its fragment.

For each detection method of the present invention, a kit is provided. The kit comprises a lysine 2-hydroxyisobutyrylation specific affinity reagent of the present invention. The kit may further comprise an instruction directing how to carry out the method.

A fusion protein reporter is provided. The fusion protein reporter comprises a core flanked by a donor fluorescent moiety and an acceptor fluorescent moiety. The core includes a peptide, which comprises a lysine 2-hydroxyisobutyrylation site and a lysine 2-hydroxyisobutyrylation binding domain. The term “lysine 2-hydroxyisobutyrylation binding domain” used herein refers to a region in a protein sequence capable of specific binding to the lysine 2-hydroxyisobutyrylation site.

The fusion protein reporter of the present invention may be useful for determining protein lysine 2-hydroxyisobutyrylation level in a sample or screening for an agent that regulates protein lysine 2-hydroxyisobutyrylation by using the fluorescence resonance energy transfer (FRET). The FRET involves the transfer of photonic energy between fluorophores when in close proximity. Donor fluorescent moieties and acceptor fluorescent moieties suitable for FRET are known in the art. In the fusion protein reporter, the donor fluorescent moiety may be selected from the group consisting of cyan fluorescent protein (CFP), enhanced cyan fluorescent protein (ECFP), and A206K mutants thereof, and the acceptor fluorescent moiety may be selected from the group consisting of yellow fluorescent protein (YFP), enhanced yellow fluorescence protein (EYFP), Citrine, Venus, and A206K mutants thereof.

The peptide in the fusion protein reporter may comprise a peptide of the present invention. It may be derived from a histone protein or fragment comprising a lysine 2-hydroxyisobutyrylation site, where the histone protein or fragment may be 2-hydroxyisobutyrylated or not at the lysine 2-hydroxyisobutyrylation site.

The lysine 2-hydroxyisobutyrylation site may be located in the N-terminus, C-terminus or the core region of a histone protein. The N-terminus, C-terminus, and core regions of histone proteins (e.g., human or mouse H1.2, H2A, H2B, H3 or H4) are known in the art.

The fusion protein reporter may comprise one or more lysine 2-hydroxyisobutyrylation binding domains. A lysine 2-hydroxyisobutyrylation binding domain may be derived from a lysine 2-hydroxyisobutyrylation specific affinity reagent of the present invention.

In some embodiments, the lysine 2-hydroxyisobutyrylation site in the peptide is not 2-hydroxyisobutyrylated, and the lysine 2-hydroxyisobutyrylation binding domain specifically binds to the lysine 2-hydroxyisobutyrylation site when the site is 2-hydroxyisobutyrylated, but not when the sites is not 2-hydroxyisobutyrylated.

In other embodiments, the lysine 2-hydroxyisobutyrylation site in the peptide is 2-hydroxyisobutyrylated, and the lysine 2-hydroxyisobutyrylation binding domain specifically binds to the lysine 2-hydroxyisobutyrylation site when the peptide is not lysine 2-hydroxyisobutyrylated, but not when the site is 2-hydroxyisobutyrylated.

The lysine 2-hydroxyisobutyrylation site may be conjugated to the lysine 2-hydroxyisobutyrylation binding domain with a linker molecule. The linker molecule may be a peptide have any amino acid sequence, and may have about 1-50 amino acids, preferably 1-30 amino acids, more preferably 2-15. In some embodiments, the linker molecule may be -Gly-Gly-. The length and contents of a linker molecule may be adjusted to optimize potential fluorescence resonance energy transfer (FRET) between the donor fluorescent moiety and the acceptor fluorescent moiety when the lysine 2-hydroxyisobutyrylation site in the fusion protein reporter is 2-hydroxyisobutyrylated or not, and bound by the lysine 2-hydroxyisobutyrylating binding domain.

The fusion protein reporter may further comprise a targeting polypeptide. The targeting polypeptide may be selected from the group consisting of a receptor ligand, a nuclear localization sequence (NLS), a nuclear export signal (NES), a plasma membrane targeting signal, a histone binding protein, and a nuclear protein.

A method for determining the level of protein lysine 2-hydroxyisobutyrylation in a sample. The method comprises detecting a 2-hydroxyisobutyrylated lysine in the sample. The method may comprise (a) contacting the sample with a fusion protein reporter of the present invention, and (b) comparing the level of fluorescence resonance energy transfer (FRET) between the donor fluorescent moiety and the acceptor fluorescent moiety after contacting with that before contacting. The level of FRET indicates the level of protein lysine 2-hydroxyisobutyrylation in the sample. The level of FRET may be increased or decreased after contacting.

A method for determining the level of protein de-lysine-2-hydroxyisobutyrylation in a sample is also provided. The method comprises (a) contacting the sample with a fusion protein reporter of the present invention, and (b) comparing the level of fluorescence resonance energy transfer (FRET) between the donor fluorescent moiety and the acceptor fluorescent moiety after contacting with that before contacting. The level of FRET indicates the level of protein de-lysine-2-hydroxyisobutyrylation in the sample. The level of FRET may be increased or decreased after contacting.

For the determination method of the present invention, a sample may be a biological sample (e.g., bodily fluid or serum). The biological sample may comprise a cell, a tissue biopsy, or a clinical fluid. The biological sample may be obtained from a subject (e.g., a mouse, rat, or human). The subject is healthy. The subject may have suffered from or may be predisposed to a protein lysine 2-hydroxyisobutyrylation or de-lysine-2-hydroxyisobutyrylation related disorder, which may be any disorder or disease linked to abnormal regulation of protein lysine 2-hydroxyisobutyrylation or de-lysine-2-hydroxyisobutyrylation, respectively. Examples of such disorder or disease may include cancer, neurodegenerative diseases, aging, metabolic disorder, and dysgenesis.

The determination method of the present invention may further comprise comparing the FRET level in the sample with a control FRET level. The control FRET level may be the FRET level in a control sample obtained from a subject, who is healthy or has not suffered from or predisposed to a protein lysine 2-hydroxyisobutyrylation related disorder. The FRET level in the sample may be higher or lower than the control FRET level.

The determination method of the present invention may further comprise adding an agent to the sample. In some embodiments, the agent is known to promote or inhibit protein lysine 2-hydroxyisobutyrylation. In other embodiments, the agent is a screening candidate for a regulator of protein lysine 2-hydroxyisobutyrylation. The screening candidate may be a compound or a biological molecule.

For each determination method of the present invention, a kit is provided. The kit comprises a fusion protein of the present invention. The kit may further comprise an instruction directing how to carry out the method.

A kit for isolating a peptide containing a 2-hydroxyisobutyrylated lysine is also provided. The kit comprises an isolated lysine 2-hydroxyisobutyrylation specific affinity reagent capable of binding specifically to a peptide comprising a 2-hydroxyisobutyrylated lysine.

A method for treating or preventing a protein lysine 2-hydroxyisobutyrylation related disease in a subject in need thereof is provided. The method comprises administering to the subject an effective amount of a composition comprising an agent that regulates protein lysine 2-hydroxyisobutyrylation. The agent may be a screen candidate identified by a determination method of the present invention. The protein lysine-2-hydroxyisobutyrylation may be histone lysine-2-hydroxyisobutyrylation.

A method for treating or preventing a protein or de-lysine-2-hydroxyisobutyrylation related disease in a subject in need thereof is provided. The method comprises administering to the subject an effective amount of a composition comprising an agent that regulates protein de-lysine-2-hydroxyisobutyrylation. The agent may be a screen candidate identified by a determination method of the present invention. The protein de-lysine-2-hydroxyisobutyrylation may be histone de-lysine-2-hydroxyisobutyrylation.

Example 1 Materials Cell Culture and Synchronization.

HeLa cells were cultured in DMEM containing 10% FBS, 1% penicillin/streptomycin at 37° C., 5% CO₂. HeLa cells were arrested at G2/M phase by a thymidine-nocodazole block. Briefly, at 50% confluency, HeLa cells were treated with 2 mM thymidine (Sigma, St Louis, Mo., USA) for 24 hours. After releasing cells from the thymidine block for 3 hours, Nocodazole (Sigma, St Louis, Mo., USA) with a final concentration of 100 ng/ml was added for another 12 hours. The dish was gently shaken and the medium containing the mitotic cells were collected. The cells were washed with cold 1×PBS (137 mmol/L NaCl, 2.7 mmol/L KCl, 10.0 mmol/L Na₂HPO₄, 1.76 mmol/L NaH₂PO₄, pH=7.4) for 3 times and used for further downstream experiments.

SILAC Labeling.

The SILAC media is formulated with SILAC Flex media supplemented with 10 ml 200 g/liter glucose, 10 ml 200 mM L-glutamine, 1.5 ml 10 g/L Phenol Red solution, 100 ml Dialyzed FBS, 10 ml 100× penicillin-Streptomycin, and 100 mg/L ¹³C₆-L-lysine.HCl or 100 mg/liter non-labeled ¹²C₆-L-lysine.HCl. The Final volume is 1 L after the above required components have been added. All reagents were purchased from Invitrogen. The media were sterile filtered. Cells were washed with 1×PBS buffer prior to exposure to SILAC Flex media. Cells were passaged 1:3 through dissociation in 0.25% trypsin. In the HeLa cells synchronization experiment, the thymine was dissolved in water without lysine and nocodazole was dissolved in DMSO without lysine. HeLa Cells underwent many passages before synchronization to achieve high isotopic amino acid incorporation. The incorporation efficiency was determined by mass spectrometry.

Chemical Propionylation.

Chemical propionylation before trypsin digestion procedure was showed as below: To 1.0 mg of histone sample dissolved in 300 μL of 0.1 M NH₄HCO₃ buffer (pH=8.0), 5.0 μL propionic anhydride was added. The pH of mixture was adjusted to keep pH between 8 and 9 by addition of 1 M NaOH with instant monitor. When the pH didn't decrease to below 8, another 5.0 μL propionic anhydride was added, and the pH of mixture was still kept pH between 8 and 9 by addition of 1 M NaOH until the pH didn't decrease. The propionylated histones were digested with trypsin (histone: trypsin=20:1) and used for immunoprecipitation. In chemical propionylation after trypsin digestion procedure, 20 μL instead of 5.0 μL propionic anhydride was used in each step.

Immunoprecipitation.

Briefly, anti-K_(2ohibu) (PTM Biolabs, Inc. (Chicago, Ill.)), anti-K_(cr) or anti-K_(ac) antibodies was first immobilized to prewashed protein A agarose beads (GE Healthcare Biosciences, Pittsburgh, Pa.) at a density of 5 mg of antibody per ml drained beads. The tryptic peptides in NH₄HCO₃ solution were incubated with 15 μL antibody immobilized protein A beads at 4° C. overnight with gentle shaking. After incubation, the beads were washed three times with NETN buffer (50 mM Tris.HCl [pH 8.0], 100 mM NaCl, 1 mM EDTA, 0.5% NP40), twice with ETN buffer (50 mM Tris.HCl [pH 8.0], 100 mM NaCl, 1 mM EDTA) and once with water. The bound peptides were eluted from the beads by washing three times with 30 μL of 0.1 M glycine solution (pH=2.5). The elutes were combined and dried in a SpeedVac.

Results Identification of a Mass Shift of +86.0354 Da at a Histone Lysine Residue

In order to discover new histone PTMs, the histone proteins from mouse spermatogenic cells, where a unique and genome-wide chromatin remodeling occurs, were digested with trypsin and the resulting tryptic peptides were analyzed by HPLC/MS/MS. The acquired MS/MS data was analyzed by the PTMap software, a non-restrictive sequence alignment algorithm that enables to detect a mass shift caused by a PTM. The analysis identified a modified H4 peptide, DAVTYTEHAKR, containing a mass shift of +86.0354 Da at its lysine residue (or H4K77). The only reasonable elemental composition responsible for this mass shift was C₄H₇O₂ (mass shift plus one proton) using ±0.02 Da mass tolerance and a maximum of 2 nitrogen atoms. According to the formula, we proposed five possible structures for the lysine modification: 2-hydroxyisobutyryl (K_(2ohibu)), 2-hydroxybutyryl (K_(2ohbu)), 3-hydroxybutyryl (K_(3ohbu)), 3-hydroxyisobutyryl (K_(3ohibu)) and 4-hydroxybutyryl (K_(4ohbu)) groups (FIG. 1).

The Mass Shift of +86.0354 Da is Caused by K_(2ohibu)

It is generally accepted that, if two peptides have the same MS/MS fragmentation patterns and are indistinguishable in HPLC chromatographic profiles, they have identical structures. To determine which of the five structure isomers is responsible for the mass shift, we first synthesized five Fmoc-protected lysine derivatives each bearing one of the five possible modifications. We then used them for the synthesis of five peptides that have the same peptide sequence (DAVTYTEHAKR) (SEQ ID NO: 29), but the different hypothesized modifications added at lysine residues, respectively.

We analyzed these synthetic peptides as well as the in vivo peptide by high-resolution MS. The MS/MS spectrum of the in vivo peptide (FIG. 2A) matched exactly with four of the synthetic peptides: DAVTYTEHAK_(2ohibu)R (FIG. 2A), DAVTYTEHAK_((±)-2ohbu)R, DAVTYTEHAK_((r)-3ohbu)R and DAVTYTEHAK_((s)-3ohibu). However, the MS/MS spectrum of the 4-hydroxybutyrylated peptide (DAVTYTEHAK_(4ohbu)R) had a significant neutral loss peak resulting from a weight loss of 86.03 Da based on its calculated molecular weight, leading to a different spectrum from that of the in vivo peptide. Thus, we concluded that the PTM in the in vivo peptide is not lysine 4-hydroxybutyrylation.

Theoretically, two peptides with the same amino acid sequence and enantiomeric groups at the same PTM site will have the same retention times on a nonchiral HPLC column. This conclusion was confirmed in our co-elution experiment using the peptides DAVTYTEHAK_((r)-3ohbu)R and DAVTYTEHAK_((s)-3ohbu)R. Therefore, in subsequent co-elution experiments, the use of racemic or enantiomeric peptides should have no influence on the co-elution results. To examine HPLC chromatographic profiles of the four synthetic peptides, we mixed the four remaining synthetic peptides (DAVTYTEHAK_(2ohibu)R, DAVTYTEHAK_((±)-2ohbu)R, DAVTYTEHAK_((r)-3ohbu)R, and DAVTYTEHAK_((s)-3ohibu)R) together with the in vivo one. The HPLC/MS/MS results revealed that these four peptides had different retention times and could be distinguished from the in vivo peptide bearing a mass shift of +86.0354 Da in the HPLC system (FIG. 2B). Accordingly, the pair-wise co-elution experiments can be used to determine the four putative structures.

Among the four possible structures, we found that the in vivo peptide co-eluted perfectly with the synthetic 2-hydroxyisobutyrylated peptide DAVTYTEHAK_(2ohibu)R (FIG. 2C). However, the other three synthetic peptides, DAVTYTEHAK_((±)-2ohbu)R, DAVTYTEHAK_((r)-3ohbu)R, and DAVTYTEHAK_((s)-3ohibu)R, did not co-elute with the in vivo peptide. These results indicate that the mass shift of the in vivo peptide is caused by K_(2ohibu) instead of lysine 2-hydroxybutyrylation, 3-hydroxybutyrylation, and 3-hydroxyisobutyrylation. Together, the MS/MS and HPLC co-elution experiments demonstrated that the mass shift of +86.0354 Da at the lysine residue of the peptide DAVTYTEHAKR is caused by K_(2ohibu).

To further confirm the new modification K_(2ohibu), we examined an additional peptide, VTIMPK_(+86.03)DIQLAR (SEQ ID NO: 47) with a mass shift of +86.03 Da, which were derived from mouse spermatogenic cells histones H3. These experiments again unambiguously demonstrated that the mass shift of +86.03 Da was caused by K_(2ohibu). Taken together, we tested the five possible structures of a lysine PTM caused by a mass shift of +86.03 Da in three in vivo peptides by MS/MS and HPLC co-elution experiments. Our results clearly showed that the mass shift of +86.03 Da at histone lysine residues is caused by K_(2ohibu).

Verification of Histone K_(2ohibu) by Western Blotting

To corroborate the new PTM, we generated a pan anti-K_(2ohibu) antibody and a sequence-specific antibody against H4K8_(2ohibu). Both antibodies have good specificities based on dot-spot assays. Using Western blot, we specifically detected K_(2ohibu) signal among all the HeLa cells core histone proteins. Likewise, using anti-H4K8_(2ohibu) antibody, we detected H4K8_(2ohibu) in HeLa cell histones, but not recombinant H4 (FIG. 3A). These results clearly demonstrate the existence of K_(2ohibu) on human histones.

Histone K_(2ohibu) is an Evolutionarily Conserved Mark

Using the pan anti-K_(2ohibu) and sequence-specific anti-H4K8_(2ohibu) antibodies, we detected K_(2ohibu) on histones not only from HeLa cells, but also from mouse embryonic fibroblast (MEF) cells, Drosophila S2 cells and yeast S. cerevisiae cells (FIG. 3B). This result clearly indicates that K_(2ohibu) is an evolutionarily-conserved in eukaryotic cells. To identify histone K_(2ohibu) sites, we used an affinity-directed MS method, involving tryptic digestion of the extracted histones from the cells of interest, enrichment of K_(2ohibu) peptides with anti-K_(2ohibu) antibody, HPLC/MS/MS analysis and protein sequence database search. This study led to identification of 60 histone K_(2ohibu) sites in mouse male germ cells (Table 1) and 22 histone K_(2ohibu) sites in HeLa cells (Table 2).

Several interesting features were observed among histone K_(2ohibu) sites. First, we detected 63 K_(2ohibu) sites in human and mouse histones. For 27 of these 63 sites, neither acetylation nor crotonylation had been reported by the research community (FIG. 3D). Second, K_(2ohibu) is located not only in N-terminal domains but also in other regions of core histones, a profile different from K_(ac). As an example, eight K_(2ohibu) sites were found to be located in the H2B globular domain between lysine 34 to lysine 120. We further examined the locations of K_(2ohibu) lysine residues in the H2B core region and found that they are precisely located at surfaces involved in inter- or intra-nucleosome interactions in mouse spermatogenic cells (FIG. 3C). For example, H2BK43 in the L1 loop, H2BK85 in the L2 loop and H2BK34 are in direct contact with DNA. Accordingly, a change of charge state from positive (protonated amine group) to neutralized state (2-hydroxyisobutyrylated lysine) is highly likely to impact the association of H2B with DNA. These observations suggest different roles of histone K_(2ohibu) from histone K_(ac) and K_(cr) in the regulation of chromatin structure and function. More interestingly, the occurrence of these nucleosome-destabilizing PTMs in the mouse spermatogenic cells is indicative of their potential role in the large-scale nucleosome disassembly that takes place in the post-meiotic cells.

To determine the stoichiometry of histone K_(2ohibu) marks, we analyzed tryptic digests of core histones from unsynchronized and synchronized HeLa cells using a Stable isotope labeling by amino acids in cell culture (SILAC)-based method. Table 5 shows the absolute stoichiometry analysis of K_(2ohibu) sites during mitosis. The stoichiometries of histone K_(2ohibu) sites were calculated based on a previously published method which requires the quantification ratios of proteins, K_(2ohibu) peptides and the corresponding unmodified tryptic peptides. Both K_(2ohibu) peptides and protein quantification ratios were measured by Maxquant (v1.0.13.13) and the protein ratios were calculated using only unmodified peptides. The quantification ratios of the corresponding unmodified tryptic peptides were based on the Maxquant quantification ratios of the longest completely-cleaved tryptic form of K_(2ohibu)-bearing peptides. We were able to determine stoichiometry of four K_(2ohibu) sites, H3K79, H2BK108, H4K91 and H1.2K63. Their stoichiometry reaches to 5.33% and 7.79% for H4K91 and H1.2K63, respectively, in the cells that were synchronized to G2/M phase. Stoichiometries for many K_(ac) and methylation sites are lower than a few percentages. As an example, it was reported that the abundance of histone H3 lysine 56 acetylation (H3K56), a histone mark with a role in genomic stability, is less than 0.1%. Our results suggest that the abundance of histone K_(2ohibu) marks is likely to be in line with that of histone acetylation and methylation marks with low to medium abundance.

Labeling of Histone K_(2ohibu) Marks by Isotopic 2-Hydroxyisobutyrate

The short-chain acyl-CoAs are the donor molecules for lysine acylations, e.g., acetyl-CoA for K_(ac) reaction. Thus, most likely, 2-hydroxyisobutyryl-CoA is the cofactor for K_(2ohibu) reaction. 2-Hydroxyisobutyryl-CoA is an intermediate in bacteria for the production of 2-hydroxyisobutyric acid, a building block for industrial polymer synthesis, and for the degradation of fuel oxygenates, methyl and ethyl tert-butyl ether, in bacteria and yeast. In human, 2-hydroxyisobutyric acid is one of the detectable organic acids that are associated with lactic acidosis.

To test if 2-hydroxyisobutyrate could be used by cells for K_(2ohibu) via 2-hydroxyisobutyryl-CoA in a similar way as cells use acetate for lysine acetylation, we treated HeLa cells with 50 mM D₆-2-hydroxyisobutyrate for 72 hours. The isotopically labeled histone K_(2ohibu) peptides were analyzed using MS. Our analysis detected D₆-labeled histone peptides. Table 6 shows the mass spectrometric analysis of the isotopic HeLa cells histone sample. The HeLa cells were treated with 50 mM D₆-2-hydroxyisobutyrate for 72 hours in DMEM medium. Only D₆-labeled K_(2ohibu) sites were shown. This result implies that 2-hydroxyisobutyryl-CoA, originated from the precursor 2-hydroxyisobutyrate, is likely the cofactor for K_(2ohibu).

Spatio-Temporal Labeling of Histone H4K8 by 2-Hydroxyisobutyrylation and Acetylation in Spermatogenic Cells

We then examined the roles of H4K8_(2ohibu) in the male germ cell specific transcriptional activities and chromatin remodeling. Indeed, our previous investigations of a critical spermatogenic factor, Brdt, specifically recognizing histone H4 lysine 5 acetylation (H4K5_(ac)) and H4K8_(ac), indicate the important function of these two H4 lysine residues, in the control of male germ cell gene expression.

Toward this goal, we first analyzed spermatogenic cells by immunohistochemistry (IH) to examine the global dynamics of H4K8_(2ohibu). The genome-wide distribution of this histone mark is dynamic and varies as a function of male germ cell differentiation (FIG. 4A). A clear labeling is observed in spermatogonia, which decreases in meiotic cells. In spermatocytes, the H4K8_(2ohibu) labeling does not show any particular pattern, while in round spermatids, H4K8_(2ohibu) forms a dot-like nuclear structure. At later stages, in elongating spermatids undergoing histone-to-transition protein (TP) replacement, the labeling becomes intense and genome-wide (FIG. 4A). Remarkably, a parallel analysis of H4K8_(ac), a mark previously studied in spermatogenic cells, revealed a similar pattern of staining as H4K8_(2ohibu) (FIG. 4B). Interestingly, the specific pattern of H4K8_(ac) labeling in round spermatids was also observed.

In order to understand the nature of the dot-like structure observed in round spermatids on the histological testis sections, we investigated the dynamics of H4K8_(2ohibu) using fluorescent immunodetection. In the mouse round spermatids, both H4K8_(2ohibu) and H4K8_(ac) marked a unique nuclear structure. In addition, the chromocenter, formed by the aggregation of all centromeric and pericentric chromosomal domains, forms a unique large heterochromatic structure, which is clearly visible by DAPI staining. The analysis of this structure with H4K8_(2ohibu) staining shows the absence of this mark from the chromocenter, but the antibody labels an adjacent structure (FIG. 4C). The co-detection of HP1gamma, known to mark both the chromocenter and the adjacent sex chromosomes, together with H4K8_(2ohibu), demonstrated that the H4K8_(2ohibu)-enriched structure corresponds to the sex chromosome, since it is absent from the chromocenter and perfectly co-localizes with the sex chromosomes. Interestingly, here again, the H4K8_(ac) mark shows a similar pattern as H4K8_(2ohibu), which is consistent with previous observations on the preferential association of this mark with sex chromosomes.

High-Resolution Genome-Wide Mapping of H4K8_(2ohibu) and H4K8_(ac) in Meiotic and Post-Meiotic Cells

To gain functional insights into histone H4K8_(2ohibu) and H4K8_(ac), we prepared nuclei from enriched meiotic (spermatocytes) and post-meiotic (round spermatids) cells and used them for a high-resolution mapping of these marks in genomic localization by ChIP-seq. Our study shows that both marks are dynamic and that there is a significant re-distribution of H4K8_(2ohibu) peaks between spermatocytes and round spermatids (FIG. 5A, upper). In addition, more than half of H4K8_(ac) peaks are associated with nucleosomes bearing H4K8_(2ohibu) mark (FIG. 5A, bottom).

The sex chromosomes (mainly the X) have a distinct global peaks distribution, where both marks are depleted compared to the autosomes, especially in spermatocytes (FIGS. 5C and 5D). This observation suggested that H4K8_(2ohibu), like H4K8_(ac), could be associated with the transcriptional activity of the chromosomes and that the relative depletion of these marks, on the X chromosome in spermatocytes, could be linked to the sex chromosome inactivation in these cells. Interestingly, in agreement with the immunodetection data, an increase of H4K8_(2ohibu) peaks was observed on the X chromosome after the completion of meiosis (FIG. 5D). A similar phenomenon was observed for H4K8_(ac), although with a much lesser degree than H4K8_(2ohibu) (FIG. 5C).

Depletion of H4K8_(ac) in the sex chromosomes in meiotic and post-meiotic cells is generally associated with the transcriptional silencing of the chromosomes. The similar observation for the depletion of H4K8_(2ohibu) in spermatogenic cells suggests an association of this histone mark with gene expression. Indeed, a metagene analysis supported this hypothesis, showing that H4K8_(2ohibu) and H4K8_(ac) are both enriched at the transcriptional start sites (TSSs) of genes (FIG. 5B). Therefore, this result highlights H4K8_(2ohibu)'s possible roles in transcriptional control.

Epigenetic Gene Signposting by H4K8_(2ohibu) and H4K8_(ac) in Meiotic and Post-Meiotic Cells

These data prompted us to examine the gene-containing fractions of the genome that are associated with these two marks. H4K8_(2ohibu) peaks were found associated to 8855 genes in meiotic or post-meiotic spermatogenic cells (FIG. 6A). In both spermatocytes and in round spermatids, only a minor fraction of genes was associated with nucleosomes bearing H4K8_(ac) alone, while the vast majority of the H4K8_(ac)-associated genes (93%) were co-localized in the genome with H4K8_(2ohibu) (FIG. 6A). The gene expression patterns of the genes marked by H4K8_(2ohibu), either alone or with H4K8_(ac) (43% and 57% of H4K8_(2ohibu)-associated genes, respectively) were analyzed using transcriptomic data derived from normal mouse tissues (data available on the GEO website, GSE10744, GSE9954, GSE4193 and GSE21749), as previously described. Briefly, within the list of genes found associated with H4K8_(2ohibu), we looked for those preferentially expressed in testis compared to other tissues. This study showed that 29% the H4K8_(2ohibu)-associated genes are testis-specific, and include meiotic and post-meiotic genes (FIGS. 6B and 6C).

Next, we examined if the genes associated with these two marks, alone or in combination, would show different transcriptional activities. To do so, stage-specific spermatogenic transcriptomes were downloaded (from the same studies as described above) and the mean expression levels of the gene categories associated with one or two marks were calculated. In spermatocytes, the expression levels of the genes bearing H4K8_(2ohibu) alone are higher than those bearing none of the two H4K8 histone marks (FIG. 6D). In addition, combination of both marks slightly increases the effect. Unexpectedly, in round spermatids, H4K8_(ac)-marked genes do not show a different transcriptional activity compared to genes devoid of the two marks, which is different from our observations in spermatocytes (FIG. 6D, right). Interestingly, in these cells, the association of H4K8_(2ohibu) alone with genes appeared as a strong indicator of a higher transcriptional activity and a combination of both marks further enhance gene expression.

Because of the relative enrichment of H4K8_(2ohibu) in the post-meiotic sex chromosomes observed by both ChIP-seq and immunodetection, we wondered if there could be a relationship between H4K8_(2ohibu) and histone crotonylation, a histone mark that has previously been shown increased on the sex chromosomes in post-meiotic cells. Interestingly, nearly no sex-linked gene was found associated with H4K8_(ac) alone (FIG. 6E, right panel), despite a moderate enrichment of this mark in post-meiotic sex chromosomes and its apparent concentration on the sex chromosomes by immunodetection observed by us here and by others. Moreover, a relatively low proportion of sex chromosome-linked genes (18%) were associated with H4K8_(2ohibu), while, in contrast, this mark was present on half of the autosomal genes (FIG. 6E, left panel). Interestingly, nearly all sex chromosome-linked genes associated with H4K8_(2ohibu) were also included in the list of genes associated with histone crotonylation, where a pan—instead of sequence-specific anti-H4K8_(cr) antibody was used. Taking into account the fact that no histone acetylation was found associated with these genes, this observation suggests that histone K_(2ohibu), could be actually more directly involved than acetylation in activating the expression of at least a fraction of these genes in round spermatids, in the repressive context of the sex chromosomes.

DISCUSSION

In this study, we identified the in vivo histone K_(2ohibu) as a new histone mark. This PTM was robustly validated by (i) MS/MS analysis, (ii) HPLC co-elution, and (iii) Western blotting using pan and sequence-specific anti-K_(2ohibu) antibodies. We subsequently identified 63 K_(2ohibu) sites in histones, including 60 sites in mouse spermatogenic cells and 22 sites in human HeLa cells, more than the total number of histone K_(ac) sites. Therefore, these histone K_(2ohibu) sites add new elements to “histone language” and significantly enhance its complexity.

Diverse differences were observed among K_(2ohibu) K_(ac) and K_(cr). First, the three histone marks show different patterns in different spermatogenic stages. These differences were consistently observed using ChIP-seq experiment. The immunostaining demonstrated that the histone H4K8_(2ohibu) mark does not show any particular pattern in spermatocytes, but forms a dot-like nuclear structure in round spermatids cells, before becoming genome-wide at the time of histone replacement. Thus, K_(2ohibu) is not only functionally distinct from K_(ac), but also has regulatory mechanisms different from those of K_(ac).

Second, K_(2ohibu), K_(ac) and K_(cr) are located at different residues of histones (FIG. 3C). Our study identified 63 histone K_(2ohibu) marks, more than the number of known histone K_(ac) marks. The K_(2ohibu) not only exists at the N-termini of the histones, but also at their main globular domains, while the majority of known K_(cr) and K_(ac) occur at the N-termini of the histones. Importantly, the stoichiometry of four K_(2ohibu) sites (H3K79, H2BK108, H4K91 and H1.2K63) is comparable or even higher than that of many histone K_(ac) marks with known biological functions.

Third, K_(ac) and K_(2ohibu) mark different groups of genes in spermatocytes. Interestingly, our study of genes associated with H4K8_(2ohibu) show that this mark is a better indicator of their transcriptional activity in post-meiotic round spermatids than the acetylation at the same position.

Fourth, K_(2ohibu) is structurally very different from lysine methylation, K_(ac), or K_(cr). Table 7 shows a comparison of changes of charge status, size, hydrophobicity caused by lysine, lysine dimethylation, K_(ac), K_(2ohibu) and K_(cr). The hydrophobicity is determined based on calculated Log P value using Chemdraw software, in which the protonated residues were used for unmodified lysine and dimethylated lysine residues. “+” means a tendency to increase. “−” means a tendency to decrease. K_(2ohibu) not only neutralizes the positive charge of lysine, but also induces much large change of its size. More importantly, K_(2ohibu) has a hydroxyl group that enables the modified lysine to form hydrogen bonds with other molecules. Such a hydroxyl group is known to be important for the regulation of protein functions, e.g., HIF1.

Finally, K_(2ohibu) is likely to result from the use of 2-hydroxyisobutyryl-CoA. Cellular metabolism has been suggested to be closely linked with epigenetic mechanisms. Thus, the K_(2ohibu) pathway could provide an opportunity for cells to reprogram epigenetics networks through histone modifications, in response to the dynamic change of a cellular metabolite, 2-hydroxyisobutyryl-CoA.

A detailed analysis of H4K8_(2ohibu) in parallel with H4K8_(ac) allowed us to highlight a new epigenetic determinant of transcriptional activation. Indeed, when we consider the gene fraction of our ChIP-seq data, we found that H4K8_(2ohibu) is a major mark associated with gene transcriptional activity and that H4K8_(ac)-bearing genes are largely included in this category constituting a sub-population of the H4K_(2ohibu)-labelled genes. Interestingly, in post-meiotic cells, H4K8_(2ohibu), but not H4K8_(ac) alone, indicates gene activity and the addition of H4K8_(ac) is associated to a group of genes with higher activity. These observations suggest that the major transcription-associated mark in the post-meiotic spermatogenic cells is unexpectedly not H4K8_(ac) but H4K8_(2ohibu). This hypothesis receives strong support from a precise analysis of the situation of the sex chromosomes. Indeed, the chromosome-wide transcriptional inactivation that occurs in meiotic cells is found here associated with a depletion of both marks, in agreement with their involvement in gene activity.

However, we also show here that in post-meiotic round spermatids, H4K8_(2ohibu), but not H4K8_(cr), becomes associated with a faction of X-linked genes that is also labeled with histone crotonylation. There might be in fact a functional redundancy between H4K8_(2ohibu) and K_(cr) in this process. However, since pan anti-K_(cr) antibody was used in the previous ChIP-seq study, some specific histone K_(cr) sites other than H4K8, may mark similar genomic locations as histone H4K8_(2ohibu). Based on these observations, we propose that H4K_(2ohibu), although functionally similar to H4K8_(ac) in terms of transcriptional activation, is of much wide use and ensures unique functions when gene activation needs to take place under general repressive conditions.

Another interesting observation is the disparity between ChIP-seq data and immunostaining data obtained in the post-meiotic sex chromosomes with anti-H4K8_(2ohibu) and H4K8_(ac) antibodies. Indeed, intense labeling of the sex chromosomes with the two histone marks was detected on testis sections by IH or by IF on seminiferous tubule sections. However, ChIP-seq data show that, although these marks are relatively enriched on the post-meiotic compared to the meiotic sex chromosomes, they remain relatively depleted on these chromosomes compared to the autosomes. Interestingly, the apparent enrichment of H4K8_(ac) in the post-meiotic sex chromosomes observed by in situ staining has been previously described. This may be caused by a specific 3D organization of the sex chromosomes in round spermatids, which would create a local region with a high density of histone marks or with chromatin organization-dependent histone marks exposed for antibody recognition. We had previously described a similar phenomenon regarding the macroH2A histone variant. While the inactive X chromosome was intensely-labeled with anti-macroH2A antibodies, the enrichment of this histone variant on the X chromosome-linked genes was only moderate compared to autosomal genes.

The discovery of K_(2ohibu) is just the beginning of the journey to study the possible diverse functions of this new modification. Extensive study of histone K_(ac) and methylation in the past few decades has revealed their critical roles in epigenetics and transcriptional control. A similar biological potential is likely to exist for histone K_(2ohibu). In addition, given the fact that all the known histone PTMs are also present in non-histone proteins, it is anticipated that K_(2ohibu) should be present in non-histone proteins and should have nucleosome-independent functions as well. Future identification of the regulatory enzymes for K_(2ohibu) and of its non-histone substrates will accelerate the characterization of its chromosome-independent functions.

The term “about” as used herein when referring to a measurable value such as an amount, a percentage, and the like, is meant to encompass variations of ±20% or ±10%, more preferably ±5%, even more preferably ±1%, and still more preferably ±0.1% from the specified value, as such variations are appropriate.

All documents, books, manuals, papers, patents, published patent applications, guides, abstracts, and other references cited herein are incorporated by reference in their entirety. Other embodiments of the invention will be apparent to those skilled in the art from consideration of the specification and practice of the invention disclosed herein. It is intended that the specification and examples be considered as exemplary only, with the true scope and spirit of the invention being indicated by the following claims.

REFERENCES

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TABLE 1 K_(2ohibu) sites in human histone proteins Human SEQ Histone  K_(2ohibu)  ID Protein sites Peptide sequences NO H1.2 H1.2K45 ASGPPVSELITK_(2ohibu)AVAASK 30 H1.2 H1.2K51 AVAASK_(2ohibu)ER 31 H1.2 H1.2K62 SGVSLAALK_(2ohibu)K 32 H1.2 H1.2K63 K_(2ohibu)ALAAAGYDVEK 33 H1.2 H1.2K84 LGLK_(2ohibu)SLVSK 34 H1.2 H1.2K89 SLVSK_(2ohibu)GTLVQTK 35 H1.2 H1.2K96 GTLVQTK_(2ohibu)GTGASGSFK 36 H2A H2AK95 NDEELNK_(2ohibu)LLGK 37 H2B H2BK5 PEPSK_(2ohibu)SAPAPK 38 H2B H2BK46 VLK_(2ohibu)QVHPDTGISSK 39 H2B H2BK85 LAHYNK_(2ohibu)R 40 H2B H2BK108 LLLPGELAK_(2ohibu)HAVSEGTK 41 H2B H2BK116 HAVSEGTK_(2ohibu)AVTK 42 H2B H2BK120 AVTK_(2ohibu)YTSSK 43 H3 H3K23 QLATK_(2ohibu)AAR 44 H3 H3K56 YQK_(2ohibu)STELLIR 45 H3 H3K79 EIAQDFK_(2ohibu)TDLR 46 H3 H3K122 VTIMPK_(2ohibu)DIQLAR 47 H4 H4K31 DNIQGITK_(2ohibu)PAIR 48 H4 H4K77 DAVTYTEHAK_(2ohibu)R 29 H4 H4K79 _(2ohibu)KTVTAMDVVYALK 49 H4 H4K91 TVTAMDVVYALK_(2ohibu)R 50

TABLE 2 K_(2ohibu) sites in mouse histone proteins Mouse SEQ Histone  K_(2ohibu)  ID Protein sites Peptide sequences NO H1.2 H1.2K22 K_(prop)K_(2ohibu)AAK_(prop)K_(prop)PAGVR 51 H1.2 H1.2K25 K_(prop)K_(prop)AAK_(2ohibu)K_(prop)PAGVR 51 H1.2 H1.2K26 K_(prop)AAK_(prop)K_(2ohibu)PAGVR 52 H1.2 H1.2K33 K_(2ohibu)ASGPPVSELITK_(prop)AVAASK_(2ohibu) 53 H1.2 H1.2K51 K_(prop)ASGPPVSELITK_(prop)AVAASK_(2ohibu)ER 54 H1.2 H1.2K62 SGVSLAALK_(2ohibu)K 32 H1.2 H1.2K74 ALAAAGYDVEK_(2ohibu)NNSR 55 H1.2 H1.2K80 IK_(2ohibu)LGLK 56 H1.2 H1.2K84 _(prop)GILVQTK_(2ohibu)SLVSK_(prop) 34 H1.2 H1.2K96 _(prop)GILVQTK_(2ohibu)GTGASGSFK_(prop) 57 H1.2 H1.2K109 _(prop)K_(2ohibu)AASGEAK_(prop)PQAK_(prop) 58 H1.2 H1.2K116 _(prop)AASGEAK_(2ohibu)PQAK_(prop) 59 H1.2 H1.2K120 _(prop)AASGEAK_(prop)PQAK_(2ohibu)k_(prop) 60 H1.2 H1.2K128 _(prop)AK_(2ohibu)K_(prop)PAGAAK_(prop) 61 H1.2 H1.2K135 _(prop)AK_(prop)K_(prop)PAGAAK_(2ohibu)K_(prop)PK_(prop) 62 H1.2 H1.2K147 _(prop)K_(prop)ATGAATPK_(2ohibu)K_(prop) 63 H1.2 H1.2K158 _(prop)K_(prop)AK_(2ohibu)K_(prop)PAAAAVTK_(prop) 64 H1.2 H1.2K167 _(prop)K_(prop)PAAAAVTK_(2ohibu)K_(prop) 65 H1.2 H1.2K211 K_(prop)VAAK_(prop)K_(prop)K_(2ohibu) 66 H2A H2AK5, K9 GK_(2ohibu)QGGK_(2ohibu)AR 67 H2A H2AK36 K_(2ohibu)GNYSER 68 H2A H2AK74, DNK_(2ohibu)K_(2ohibu)TR 69 K75 H2A H2AK95 NDEELNK_(2ohibu)LLGR 70 H2A H2AK118 VTIAQGGVLPNIQAVLLIDK_(2ohibu)K 71 H2B H2BK5 _(prop)PEPAK_(2ohibu)SAPAPK_(prop) 72 H2B H2BK12 _(prop)PEPAK_(prop)SAPAPK_(prop)K_(2ohibu)GSK 73 H2B H2BK20 K_(prop)AISK_(2ohibu)AQK_(prop) 74 H2B H2BK23 AVTK_(prop)AQK_(2ohibu)K_(prop)DGK_(prop)K_(prop)R 75 H2B H2BK24 AVTK_(prop)AQK_(prop)K_(2ohibu)DGK_(prop)K_(prop)R 75 H2B H2BK34 K_(2ohibu)ESYSVYVYK 76 H2B H2BK43 KESYSVYVYK_(2ohibu)VLK 77 H2B H2BK46 VLK_(2ohibu)QVHPDTGISSK 39 H2B H2BK57 QVHPDTGISSK_(2ohibu)AMGIMNSFVNDIFER 78 H2B H2BK85 LAHYNK_(2ohibu)R 40 H2B H2BK108 LLLPGELAK_(2ohibu)HAVSEGTK 41 H2B H2BK116 HAVSEGTK_(2ohibu)AVTK 42 H2B H2BK120 AVTK_(2ohibu)YTSSK 43 H3 H3K4 TK_(2ohibu)QTAR 79 H3 H3K9 K_(2ohibu)STGGK_(ac)APR 80 H3 H3K14 K_(prop)STGGK_(2ohibu)APR 80 H3 H3K18 K_(2ohibu)QLATK_(ac)AAR 81 H3 H3K23 KQLATK_(2ohibu)AAR 81 H3 H3K27 K_(2ohibu)SAPATGGVK_(prop)K_(prop)PHR 82 H3 H3K36 K_(prop)SAPATGGVK_(2ohibu)K_(prop)PHR 82 H3 H3K56 YQK_(2ohibu)STELLIR 45 H3 H3K64 K_(2ohibu)LPFQR 83 H3 H3K79 EIAQDFK_(2ohibu)TDLR 46 H3 H3K122 VTIMPK_(2ohibu)DIQLAR 47 H4 H4K5 K_(2ohibu)GGK_(ac)GLGK_(ac)GGAK_(ac)R 84 H4 H4K8 GK_(ac)GGK_(2ohibu)GLGK_(ac)GGAK_(ac)R 85 H4 H4K12 GLGK_(2ohibu)GGAK_(ac)R 86 H4 H4K16 GGK_(prop)GLGK_(prop)GGAK_(2ohibu)R 87 H4 H4K31 DNIQGITK_(2ohibu)PAIR 48 H4 H4K44 RGGVK_(2ohibu)R 88 H4 H4K59 GVLK_(2ohibu)VFLENVIR 89 H4 H4K77 DAVTYTEHAK_(2ohibu)R 29 H4 H4K79 K_(2ohibu)TVTAMDVVYALK 49 H4 H4K91 KTVTAMDVVYALK_(2ohibu)R 90

TABLE 3 K_(2ohibu) sites in S. cerevisiae histone proteins S. cerevisiae SEQ Histone  K_(2ohibu)  ID Protein sites Peptide sequences NO H2A H2AK13 AGSAAK_(2ohibu)ASQSR 91 H2B H2BK37 K_(2ohibu)ETYSSYTYK 92 H2B H2BK46 ETYSSYIYK_(2ohibu)VLK 93 H2B H2BK82 IATEASK_(2ohibu)LAAYNK 94 H2B H2BK111 LILPGELAK_(2ohibu)HAVSEGTR 95 H3 H3K56 FQK_(2ohibu)STELLIR 96 H4 H4K31 DNIQGITK_(2ohibu)PAIR 48 H4 H4K77 DSVTYTEHAK_(2ohibu)R 97 H4 H4K79 K_(2ohibu)TVTSLDVVYALK 98 H4 H4K91 TVTSLDVVYALK_(2ohibu)R 99

TABLE 4 K_(2ohibu) sites in Tetrahymena macronuclear   histone proteins Tetrahymena SEQ Histone  ID Protein K_(2ohibu) sites Peptide sequences NO H4 H4K11 GMGK_(2ohibu)VGAK 100 H4 H4K79 K_(2ohibu)TVTAMDVVYALK  49 H4 H4K91 TVTAMDVVYALK_(2ohibu)R  50 H3 H3K27 K_(2ohibu)SAPATGGIK 101 H3 H3K56 YQK_(2ohibu)STDLLIR 102 H3 H3K64 K_(2ohibu)LPFQR  83 H3 H3K122 VTIMTK_(2ohibu)DMQLAR 103 H2B H2BK4 K_(2ohibu)APAAAAEK 104 H2B H2BK12 K_(ac)APAAAAEK_(2ohibu)K 105 H2B H2BK41 VLK_(2ohibu)QVHPDVGISK 106 H2B H2BK74 IALESSK_(2ohibu)LVR 107 H2B H2BK111 HAISEGTK_(2ohibu)AVTK 108 H2B H2BK115 AVTK_(2ohibu)FSSSTN 109 H2A H2AK17 TASSK_(2ohibu)QVSR 110

TABLE 5 Absolute stoichiometry analysis of K_(2ohibu)  sites during mitosis. Stoichiometry of K_(2ohibu)  Stoichiometry of K_(2ohibu) K_(2ohibu)  in unsynchronized  in G2/M phase sites Peptide sequences HeLa cells HeLa cells H3K79 EIAQDFK_(2ohibu)TDLR 0.60% 1.45% H2BK108 LLLPGELAK_(2ohibu)HAVSEGTK 0.64% 1.54% H4K91 TVTAMDVVYALK_(2ohibu)R 3.16% 5.33% H1.2K63 SGVSLAALK_(2ohibu)K 3.34% 7.79%

TABLE 6 Mass spectrometric analysis of the isotopic HeLa cells histone sample. D₆-labeled K_(2ohibu) sites Peptide sequences SEQ ID NO H2AK7 AGGK_(ac)AGK_(2ohibu)DSGK 111 H2AK4 AGGK_(2ohibu)AGK_(ac)DSGK 111 H4K8 GGK_(2ohibu)GLGK_(ac)GGAK_(ac)R  87 H4K12 GGK_(ac)GLGK_(2ohibu)GGAK_(ac)R  87 H4K12 GLGK_(2ohibu)GGAK_(ac)R  86 H3K23 K_(ac)QLATK_(2ohibu)AAR  81 H2BK5 PEPAK_(2ohibu)SAPAPK  72 H2BK11 SAPAPK_(2ohibu)K_(ac)GSK 112

TABLE 7 A comparison of changes of charge status, size, hydrophobicity caused by lysine, lysine dimethylation, K_(ac), K_(2ohibu) and K_(cr). PTMs                       comparison           K:  

        K_(me2):  

    K_(ac):  

    K_(2ohibu):  

K_(cr):  

pl 0 + − − − Size 0 + + +++ ++ Hydrophobicity 0 +++ + ++ ++++ 

What is claimed:
 1. An isolated peptide comprising a 2-hydroxyisobutyrylated lysine.
 2. The isolated peptide of claim 1, wherein the peptide is derived from a histone protein or a fragment thereof.
 3. The isolated peptide of claim 2, wherein the histone protein is derived from an organism selected from the group consisting of human, mouse, S. cerevisiae, Tetrahymena thermophila, D. melanogaster, and C. elegans.
 4. The isolated peptide of claim 1, wherein the peptide comprises an amino acid sequence having at least 70% identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 29-112.
 5. The isolated peptide of claim 1, wherein the peptide comprises an amino acid sequence selected from SEQ ID NOs: 29-112.
 6. The isolated peptide of claim 1, wherein the peptide comprises at least 2 amino acid residues on each of the N-terminal and C-terminal sides of the 2-hydroxyisobutyrylated lysine.
 7. An isolated lysine 2-hydroxyisobutyrylation specific affinity reagent capable of binding specifically to the peptide of claim
 1. 8. The isolated lysine 2-hydroxyisobutyrylation specific affinity reagent of claim 7, wherein the peptide comprises an amino acid sequence selected from SEQ ID NOs: 29-112.
 9. The isolated lysine 2-hydroxyisobutyrylation specific affinity reagent of claim 7, wherein the binding is dependent on the presence of the 2-hydroxyisobutyrylated lysine but not a surrounding peptide sequence thereof in the peptide.
 10. The isolated lysine 2-hydroxyisobutyrylation specific affinity reagent of claim 7, wherein the binding is dependent on the presence of the 2-hydroxyisobutyrylated lysine and a surrounding peptide sequence thereof in the peptide.
 11. The isolated lysine 2-hydroxyisobutyrylation specific affinity reagent of claim 7, wherein the lysine 2-hydroxyisobutyrylation specific affinity reagent is a protein.
 12. A method for producing the lysine 2-hydroxyisobutyrylation specific affinity reagent of claim 11, comprising screening a protein library using a peptide comprising a 2-hydroxyisobutyrylated lysine and at least two amino acid residues on each of the N-terminal and C-terminal sides of the 2-hydroxyisobutyrylated lysine.
 13. The isolated lysine 2-hydroxyisobutyrylation specific affinity reagent of claim 7, wherein the lysine 2-hydroxyisobutyrylation specific affinity reagent is an antibody.
 14. A method for producing the lysine 2-hydroxyisobutyrylation specific affinity reagent of claim 13, comprising immunizing a host with a peptide comprising a 2-hydroxyisobutyrylated lysine and at least two amino acid residues on each of the N-terminal and C-terminal sides of the 2-hydroxyisobutyrylated lysine.
 15. A method for detecting a 2-hydroxyisobutyrylated lysine in a protein or a fragment thereof, comprising: (a) contacting the protein or a fragment thereof with the isolated lysine 2-hydroxyisobutyrylation specific affinity reagent capable of binding specifically to the peptide of claim 1, whereby the lysine 2-hydroxyisobutyrylation specific affinity reagent and the protein or a fragment thereof forms a binding complex, and (b) detecting the binding complex, wherein the presence of the binding complex indicates the presence of a 2-hydroxyisobutyrylated lysine in the protein or a fragment thereof.
 16. The method of claim 15, wherein the lysine 2-hydroxyisobutyrylation specific affinity reagent is a protein.
 17. The method of claim 15, wherein the lysine 2-hydroxyisobutyrylation specific affinity reagent is an antibody.
 18. A method for determining the level of protein lysine 2-hydroxyisobutyrylation in a sample, comprising detecting a 2-hydroxyisobutyrylated lysine in the sample.
 19. A kit for detecting a 2-hydroxyisobutyrylated lysine in a protein of a fragment thereof, comprising the isolated lysine 2-hydroxyisobutyrylation specific affinity reagent capable of binding specifically to the peptide of claim
 1. 20. A kit for isolating a peptide containing a 2-hydroxyisobutyrylated lysine, comprising the isolated lysine 2-hydroxyisobutyrylation specific affinity reagent capable of binding specifically to the peptide of claim
 1. 